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scplotter

scplotter is an R package that is built upon plotthis. It provides a set of functions to visualize single-cell sequencing data in an easy and efficient way.

Installation 

remotes::install_github("pwwang/scplotter")
# or
devtools::install_github("pwwang/scplotter")
# or using conda
$ conda install pwwang::r-scplotter

scRNA-seq

CellDimPlot

CellStatPlot

ClustreePlot | CellVelocityPlot

FeatureStatPlot

EnrichmentPlot

GSEASummaryPlot | GSEAPlot

MarkersPlot

CCCPlot (Cell-Cell Communication Plot)

scTCR-seq/scBCR-seq

ClonalVolumePlot | ClonalAbundancePlot | ClonalResidencyPlot | ClonalDynamicsPlot | ClonalCompositionPlot | ClonalOverlapPlot | ClonalGeneUsagePlot

ClonalRarefactionPlot | ClonalKmerPlot | ClonalDiversityPlot | ClonalPositionalPlot | ClonalLengthPlot | ClonalStatPlot

Spatial data

SpatDimPlot | SpatFeaturePlot

Visualization with LLMs 

provider <- tidyprompt::llm_provider_openai(api_key = Sys.getenv("OPENAI_API_KEY"))
chat <- SCPlotterChat$new(provider = provider)
chat$ask("Generate a cell-cell communication plot for the cellphonedb_res data.")
# Tool identified:  CCCPlot
# Data object identified:  cellphonedb_res
# Running tool:  CCCPlot

chat$ask("Do a heatmap instead")
# Tool identified:  CCCPlot
# Data object identified:  cellphonedb_res
# Running tool:  CCCPlot

Credits

scplotter is built upon the following fantastic packages:

  • plotthis for the core plotting functions.
  • tidyprompt for the LLM interface.
  • Seurat for the Seurat object support.
  • LIANA for the cell-cell communication analysis.
  • scRepertoire for the TCR/BCR repertoire analysis.
  • Giotto for the spatial data analysis.